def test_lint_ga_unicycler_training():
# no tags, fails linting
assert main(["lint", "--training-topic", "assembly", os.path.join(TEST_PATH, "unicycler.ga")]) == 1
# correct tag passes linting
assert main(["lint", "--training-topic", "assembly", os.path.join(TEST_PATH, "unicycler-hacked-tags.ga")]) == 0
# incorrect tag, fails linting
assert main(["lint", "--training-topic", "mapping", os.path.join(TEST_PATH, "unicycler-hacked-tags.ga")]) == 1
def test_lint_examples():
for file_name in os.listdir(TEST_LINT_EXAMPLES):
file_path = os.path.join(TEST_LINT_EXAMPLES, file_name)
expected_exit_code = int(file_name[0])
actual_exit_code = main(["lint", file_path])
if actual_exit_code != expected_exit_code:
contents = open(file_path, "r").read()
template = "File [%s] didn't lint properly - expected exit code [%d], got [%d]. Contents:\n%s"
raise AssertionError(template % (file_name, expected_exit_code, actual_exit_code, contents))
def test_lint_ecoli_comparison():
assert main(["lint", os.path.join(TEST_PATH, "ecoli-comparison.ga")]) == 1 # no outputs
def test_lint_ga_unicycler_ts_tools():
# only difference is testoolshed tool.
assert main(["lint", os.path.join(TEST_PATH, "unicycler-hacked-testtoolshed.ga")]) == 1
def test_lint_ga_unicycler_missing_tools():
# only difference is one missing tool.
assert main(["lint", os.path.join(TEST_PATH, "unicycler-hacked-no-tool.ga")]) == 1
def test_lint_ga_unicycler():
assert main(["lint", os.path.join(TEST_PATH, "unicycler.ga")]) == 0
def test_lint_ga_basic():
assert main(["lint", os.path.join(TEST_PATH, "wf3-shed-tools-raw.ga")]) == 1 # no outputs